AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_pyro_reg_300.orf -o00280_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0677 225 350aa long hypothetical acyl carrier protein synthetase #2 PH1304 119 276aa long hypothetical protein #3 PH1306 236 563aa long hypothetical methylmalonyl-CoA mutase Motif number 1 CCCCCGCTATGGCCGCCGTACCACTAACCACTCCCCAC 3 18 0 GGCGCCACAC 0.966308 -219 CCATAGCGGGGGGGTTACACCCGGTCTCATTTCGAACC 3 44 1 GGGCCCGGTC 0.999196 -193 ATCGCTGGGGGGCTTAACTTCCGGGTTCGAAATGAGAC 3 67 0 GGCCCCGGTC 0.999582 -170 CCTCTCGGAGGGCAGTACAACCGGGATCGCTGGGGGGC 3 92 0 GGCCCCGGTC 0.999577 -145 CGGCGTCCCCGGCTTCCCGCCCCCTCTCGGAGGGCAGT 3 114 0 GGCCCCCCTC 0.997165 -123 GCGGGAAGCCGGGGACGCCGCCGGCCACCCTAATTCTC 3 132 1 GGGCCCGGAC 0.997632 -105 *** * **** ** Masking position 11 Map Score: 9.98084 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 12 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 AATGATAGCATTTGACAATTGTCGTAATGTC 1 99 0 TTTGAAATTG 0.851469 -127 CGATCAACGATTTTAGATTGTACTATTACCG 1 146 1 TTTTAATTGT 0.944284 -80 TTAAGTACTATTTGAAATTGTTAAATTTGGT 2 19 0 TTTGAATTGT 0.986684 -101 TTGATTTTTATTGGATAATGTTTTTAAGTAC 2 42 0 TTGGAAATGT 0.936166 -78 TTAGATTAGTTTTGTCATTGTGTTTGATTTT 2 65 0 TTTGTATTGT 0.912482 -55 ATAAATATATTTTTAGATTAGTTTTGTCATT 2 77 0 TTTTAATTAG 0.766999 -43 TATATTTATCTTTGACATTATTTTTATAAAC 2 99 1 TTTGAATTAT 0.95286 -21 TTTAAAGAATTTGGACATTTTGTTCAAGAGA 3 166 0 TTGGAATTTT 0.953752 -71 GTCCAAATTCTTTAAATTTGTAAAGTTTTTA 3 181 1 TTTAATTTGT 0.704556 -56 TGTTTATGTGTTGAATATTTGCCCTATAAAA 3 207 0 TTGAAATTTG 0.770559 -30 ***** ***** Masking position 9 Map Score: 7.17797 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 184 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TACATATATTCGGCGATCAACGATTTTAGA 1 133 1 CGGCGATCAA 0.980173 -93 GTTAGTGGTACGGCGGCCATAGCGGGGGGG 3 28 1 CGGCGGCCAT 0.99139 -209 TTAAGCCCCCCAGCGATCCCGGTTGTACTG 3 88 1 CAGCGATCCC 0.983113 -149 GGGTGGCCGGCGGCGTCCCCGGCTTCCCGC 3 132 0 CGGCGTCCCC 0.996303 -105 GGGACGCCGCCGGCCACCCTAATTCTCTTG 3 143 1 CGGCCACCCT 0.991982 -94 ********** Masking position 4 Map Score: 4.40572 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 20 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 GTCAAATGCTATCATTACCTACATATATTC 1 114 1 ATCATTACCT 0.953976 -112 ACCTTTTCTTTTCTTCACCTATTAGCCTTT 1 198 0 TTCTTCACCT 0.99084 -28 TCTTCATCACCTTTTCTTTTCT 1 214 0 TTCATCACCT 0.99359 -12 AGGGCAAATATTCAACACATAAACAGGTGA 3 213 1 TTCAACACAT 0.900274 -24 ATTTTCACCTGTTTATGTGT 3 227 0 ATTTTCACCT 0.935338 -10 ********** Masking position 7 Map Score: 3.70784 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 124 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AATGTCTTAGTACCTCCACCGAAAACTACA 1 75 0 TACCTCCACC 0.960684 -151 GCCGTACCACTAACCACTCCCCACAAACAC 3 12 0 TAACCACTCC 0.967459 -225 AGACCGGGTGTAACCCCCCCGCTATGGCCG 3 41 0 TAACCCCCCC 0.997874 -196 ACCCGGAAGTTAAGCCCCCCAGCGATCCCG 3 79 1 TAAGCCCCCC 0.992553 -158 CGTCCCCGGCTTCCCGCCCCCTCTCGGAGG 3 119 0 TTCCCGCCCC 0.982889 -118 ********** Masking position 1 Map Score: 4.15625 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 73 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ACTCAGATTAATTGAAAGCTTAAGGGGGCA 1 17 0 ATTGAAAGCT 0.76552 -209 CATAAATCTAACTTAAAAACTCTAGATTGA 1 47 0 ACTTAAAAAC 0.940732 -179 TAGTACCTCCACCGAAAACTACATAAATCT 1 68 0 ACCGAAAACT 0.953917 -158 TAATAGTACAATCTAAAATCGTTGATCGCC 1 144 0 ATCTAAAATC 0.917216 -82 TTGTACTATTACCGAAAGTCTTTTATAAAG 1 163 1 ACCGAAAGTC 0.948977 -63 TTCAAATAGTACTTAAAAACATTATCCAAT 2 34 1 ACTTAAAAAC 0.940732 -86 GACAAAACTAATCTAAAAATATATTTATCT 2 80 1 ATCTAAAAAT 0.880957 -40 ********** Masking position 5 Map Score: 1.6802 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 154 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 TCCACCGAAAACTACATAAATCTAACTTAA 1 61 0 ACTACATAAA 0.923622 -165 GCTATCATTACCTACATATATTCGGCGATC 1 121 1 CCTACATATA 0.95044 -105 GCCTTTCAACCCTTTATAAAAGACTTTCGG 1 174 0 CCTTTATAAA 0.946465 -52 AAAACATTATCCAATAAAAATCAAACACAA 2 49 1 CCAATAAAAA 0.925389 -71 GAATATTTGCCCTATAAAAACTTTACAAAT 3 196 0 CCTATAAAAA 0.975962 -41 ********** Masking position 6 Map Score: 1.53672 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 65 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ********** No masking Map Score: 1.24588e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.24588e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 1.24588e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0